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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-06, 17:45 based on data in: /home/chengxin/pmultiqctest/test_dia/results


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 4/4 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        RD139_Narrow_UPS1_0_1fmol_inj1.mzML1111
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        RD139_Narrow_UPS1_0_1fmol_inj2.mzML2111
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        RD139_Narrow_UPS1_0_25fmol_inj1.mzML3112
        CT=Mixture;CN=UPS1;QY=0.25fmol
        2
        RD139_Narrow_UPS1_0_25fmol_inj2.mzML4112
        CT=Mixture;CN=UPS1;QY=0.25fmol
        2

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 2/2 columns.
        Total MS/MS SpectralTotal Peptide QuantifiedTotal Protein Quantified
        573300
        5729
        1605

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 4/4 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        RD139_Narrow_UPS1_0_1fmol_inj1.mzML
        1
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        5407
        5407
        871
        1552
        RD139_Narrow_UPS1_0_1fmol_inj2.mzML
        1
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        5434
        5434
        880
        1562
        RD139_Narrow_UPS1_0_25fmol_inj1.mzML
        2
        CT=Mixture;CN=UPS1;QY=0.25fmol
        1
        5572
        5572
        901
        1578
        RD139_Narrow_UPS1_0_25fmol_inj2.mzML
        2
        CT=Mixture;CN=UPS1;QY=0.25fmol
        1
        5558
        5558
        896
        1588

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        Showing 50/50 rows and 8/8 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage IntensityCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmol
        1
        TOLA_ECOLI
        AAAEADDIFGELSSGK
        0.000
        846915.750
        774334.000
        919497.500
        2
        G3P2_ECOLI
        AAAENIIPHTTGAAK
        0.000
        1342442.000
        1206361.000
        1478523.000
        3
        RLMH_ECOLI
        AAAEQSWSLSALTLPHPLVR
        0.000
        1733785.000
        1567770.000
        1899800.000
        4
        PDXJ_ECOLI
        AAAEVGAPFIEIHTGC(Carbamidomethyl)YADAK
        0.000
        251631.000
        314472.000
        188790.000
        5
        RL10_ECOLI
        AAAFEGELIPASQIDR
        0.000
        354762950.000
        320310450.000
        389215450.000
        6
        YFGM_ECOLI
        AAAQLQQGLADTSDENLK
        0.000
        4886546.250
        4987713.000
        4785379.500
        7
        YFGM_ECOLI
        AAAQLQQGLADTSDENLKAVINLR
        0.000
        1483184.000
        1076653.000
        1889715.000
        8
        RHLE_ECOLI
        AAATGEALSLVC(Carbamidomethyl)VDEHK
        0.000
        509699.750
        478474.500
        540925.000
        9
        SYP_ECOLI
        AAATQEMTLVDTPNAK
        0.000
        1923027.500
        1597805.000
        2248250.000
        10
        EUTL_ECOLI
        AAC(Carbamidomethyl)NAFTDAVLEIAR
        0.000
        426526.750
        402131.000
        450922.500
        11
        ACRB_ECOLI
        AADGQMVPFSAFSSSR
        0.000
        1192397.250
        868414.500
        1516380.000
        12
        YIDA_ECOLI
        AADGSTVAQTALSYDDYR
        0.000
        499831.000
        481552.500
        518109.500
        13
        ADHE_ECOLI
        AADIVLQAAIAAGAPK
        0.000
        47585057.500
        44369700.000
        50800415.000
        14
        NARG_ECOLI
        AADLVDALGQENNPEWK
        0.000
        493038.500
        441933.500
        544143.500
        15
        DNAK_ECOLI
        AADNKSLGQFNLDGINPAPR
        0.000
        334393.750
        313148.000
        355639.500
        16
        OXYR_ECOLI
        AADSC(Carbamidomethyl)HVSQPTLSGQIR
        0.000
        3826104.500
        3544684.000
        4107525.000
        17
        TALA_ECOLI
        AAEELEKEGINC(Carbamidomethyl)NLTLLFSFAQAR
        0.000
        1836555.000
        1606540.000
        2066570.000
        18
        HEMY_ECOLI
        AAELAGNDTIPVEITR
        0.000
        2748975.000
        2664665.000
        2833285.000
        19
        SYL_ECOLI
        AAENNPELAAFIDEC(Carbamidomethyl)R
        0.000
        9653027.000
        8733679.000
        10572375.000
        20
        TALB_ECOLI
        AAEQLEKEGINC(Carbamidomethyl)NLTLLFSFAQAR
        0.000
        9563185.000
        7875370.000
        11251000.000
        21
        MBHM_ECOLI
        AAESALNIDVPVNAQYIR
        0.000
        1359970.000
        1350170.000
        1369770.000
        22
        DNAG_ECOLI
        AAESGVSRPVPQLKR
        0.000
        130118.225
        90883.950
        169352.500
        23
        HDFR_ECOLI
        AAESLYLTQSAVSFR
        0.000
        1135141.500
        1026993.500
        1243289.500
        24
        RNE_ECOLI
        AAESRPAPFLIHQESNVIVR
        0.000
        3760450.000
        3607580.000
        3913320.000
        25
        HFLK_ECOLI
        AAFDDAIAARENEQQYIR
        0.000
        632781.000
        431945.000
        833617.000
        26
        AROF_ECOLI
        AAFPLSLQQEAQIADSR
        0.000
        845924.750
        852260.000
        839589.500
        27
        AROF_ECOLI
        AAFPLSLQQEAQIADSRK
        0.000
        577017.750
        539224.000
        614811.500
        28
        BOLA_ECOLI
        AAFQPVFLEVVDESYR
        0.000
        5357111.250
        5149619.000
        5564603.500
        29
        CLPB_ECOLI
        AAGATTANITQAIEQMR
        0.000
        1203692.750
        938926.500
        1468459.000
        30
        YBIS_ECOLI
        AAGEPLPAVVPAGPDNPMGLYALYIGR
        0.000
        917925.750
        688771.500
        1147080.000
        31
        SDHA_ECOLI
        AAGLHLQESIAEQGALR
        0.000
        264544.250
        268834.000
        260254.500
        32
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGK
        0.000
        152497.625
        130686.750
        174308.500
        33
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGKK
        0.000
        664122.000
        597449.500
        730794.500
        34
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVR
        0.000
        2939852.500
        3287255.000
        2592450.000
        35
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVRK
        0.000
        6793310.000
        5967400.000
        7619220.000
        36
        ENO_ECOLI
        AAGYELGKDITLAMDC(Carbamidomethyl)AASEFYK
        0.000
        4432855.000
        4256870.000
        4608840.000
        37
        YEBE_ECOLI
        AAHQDEPQFGAQSTPLDER
        0.000
        445723.000
        418773.500
        472672.500
        38
        RIBB_ECOLI
        AAIADGAKPSDLNRPGHVFPLR
        0.000
        2904107.500
        2699630.000
        3108585.000
        39
        DEOC_ECOLI
        AAIAYGADEVDVVFPYR
        0.000
        11244722.500
        9835005.000
        12654440.000
        40
        IDH_ECOLI
        AAIEYAIANDRDSVTLVHK
        0.000
        1937385.000
        1857390.000
        2017380.000
        41
        DPO1_ECOLI
        AAINAPMQGTAADIIKR
        0.000
        749948.750
        710673.000
        789224.500
        42
        SYFA_ECOLI
        AAISQASDVAALDNVR
        0.000
        7640428.000
        7563992.000
        7716864.000
        43
        SYFA_ECOLI
        AAISQASDVAALDNVRVEYLGK
        0.000
        1109521.500
        963013.000
        1256030.000
        44
        MUKF_ECOLI
        AAISSC(Carbamidomethyl)ELLLSETSGTLR
        0.000
        284353.000
        248315.000
        320391.000
        45
        MSCM_ECOLI
        AAKPAQPEVVEALQSALNALEER
        0.000
        183940.000
        147673.500
        220206.500
        46
        AMPN_ECOLI
        AALEQLKGLENLSGDLYEK
        0.000
        1812735.000
        1565615.000
        2059855.000
        47
        DBHA_ECOLI
        AALESTLAAITESLK
        0.000
        20094115.000
        20555690.000
        19632540.000
        48
        HEM3_ECOLI
        AALPPEISLPAVGQGAVGIEC(Carbamidomethyl)R
        0.000
        2045097.500
        1904335.000
        2185860.000
        49
        SDHA_ECOLI
        AALQISQSGQTC(Carbamidomethyl)ALLSK
        0.000
        365811.250
        300655.000
        430967.500
        50
        DHE4_ECOLI
        AANAGGVATSGLEMAQNAAR
        0.000
        539616.500
        457741.000
        621492.000
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        Showing 50/50 rows and 6/6 columns.
        ProteinNamePeptides_NumberAverage IntensityCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmol
        3PASE_ECOLI
        1
        420197.250
        402369.500
        438025.000
        5DNU_ECOLI
        1
        156098.625
        129354.250
        182843.000
        6PGD_ECOLI
        10
        26895755.250
        25958432.000
        27833078.500
        6PGL_ECOLI
        2
        3189108.750
        2965753.000
        3412464.500
        AAEB_ECOLI
        1
        1513570.000
        1383610.000
        1643530.000
        AAS_ECOLI
        4
        1171200.350
        1182410.000
        1159990.700
        AAT_ECOLI
        2
        14909300.500
        14172630.000
        15645971.000
        ABGT_ECOLI
        1
        175533.500
        213843.000
        137224.000
        ACCA_ECOLI
        11
        57522248.500
        52125747.000
        62918750.000
        ACCC_ECOLI
        12
        41384270.250
        37850097.000
        44918443.500
        ACCD_ECOLI
        4
        9053901.000
        8786082.000
        9321720.000
        ACEA_ECOLI
        10
        16144268.575
        14606640.650
        17681896.500
        ACFD_ECOLI
        8
        6756542.000
        6173109.500
        7339974.500
        ACKA_ECOLI
        10
        196682611.750
        183834543.000
        209530680.500
        ACNA_ECOLI
        5
        1293660.675
        1075347.850
        1511973.500
        ACNB_ECOLI
        11
        36175300.000
        33144922.500
        39205677.500
        ACRA_ECOLI
        6
        31432966.000
        28244059.500
        34621872.500
        ACRB_ECOLI
        6
        7385168.000
        6371148.000
        8399188.000
        ACSA_ECOLI
        2
        393878.250
        432040.500
        355716.000
        ACUI_ECOLI
        5
        10978366.625
        9084449.000
        12872284.250
        ACYP_ECOLI
        1
        411140.500
        401705.000
        420576.000
        ADD_ECOLI
        5
        19171885.000
        18025905.000
        20317865.000
        ADEC_ECOLI
        1
        244349.250
        225267.500
        263431.000
        ADHE_ECOLI
        36
        448711850.100
        407843381.000
        489580319.200
        ADHP_ECOLI
        2
        1199567.500
        1190027.000
        1209108.000
        ADIA_ECOLI
        3
        836907.750
        708293.000
        965522.500
        ADPP_ECOLI
        2
        4103438.750
        3805853.000
        4401024.500
        AGP_ECOLI
        3
        1372987.500
        1277708.500
        1468266.500
        AHPC_ECOLI
        9
        134366034.750
        125108945.000
        143623124.500
        AHPF_ECOLI
        9
        39256342.000
        37664884.500
        40847799.500
        AHR_ECOLI
        1
        116027.500
        136532.000
        95523.000
        AK1H_ECOLI
        7
        3079193.250
        2879310.950
        3279075.550
        AK2H_ECOLI
        4
        3176166.000
        2965459.500
        3386872.500
        AK3_ECOLI
        5
        3913562.750
        3440695.000
        4386430.500
        ALAA_ECOLI
        3
        4042784.000
        3814502.000
        4271066.000
        ALAC_ECOLI
        5
        3722325.100
        3247928.700
        4196721.500
        ALDB_ECOLI
        1
        1103561.250
        1024387.500
        1182735.000
        ALF1_ECOLI
        2
        381190.025
        122557.050
        639823.000
        ALF_ECOLI
        10
        136741488.050
        130700258.900
        142782717.200
        ALKH_ECOLI
        3
        4425314.250
        3703778.500
        5146850.000
        ALR1_ECOLI
        3
        4625940.000
        4270210.000
        4981670.000
        AMIA_ECOLI
        1
        643034.500
        583220.500
        702848.500
        AMIB_ECOLI
        2
        535836.250
        493469.000
        578203.500
        AMIC_ECOLI
        5
        978021.700
        787568.500
        1168474.900
        AMID_ECOLI
        1
        36307.350
        22821.400
        49793.300
        AMN_ECOLI
        8
        5829460.750
        5524845.500
        6134076.000
        AMPA_ECOLI
        7
        18453118.500
        17097292.500
        19808944.500
        AMPC_ECOLI
        2
        1318665.750
        1153699.500
        1483632.000
        AMPH_ECOLI
        2
        1433161.250
        1236562.000
        1629760.500
        AMPN_ECOLI
        7
        12792446.775
        12077266.550
        13507627.000
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        ASSEMBLE_EMPIRICAL_LIBRARY DIA-NN 1.8.1
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DIANNCFG sdrf-pipelines 0.0.21
        DIANNCONVERT sdrf-pipelines 0.0.21
        DIANNSUMMARY DIA-NN 1.8.1
        DIANN_PRELIMINARY_ANALYSIS DIA-NN 1.8.1
        INDIVIDUAL_FINAL_ANALYSIS DIA-NN 1.8.1
        MSSTATS bioconductor-msstats 4.2.0
        r-base 4.1.2
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        voluminous_thompson
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_dia,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
        outdir
        ./results_dia

        Protein database

        database
        /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta

        Database search

        allowed_missed_cleavages
        1
        instrument
        N/A
        max_precursor_charge
        3
        min_peptide_length
        15
        max_peptide_length
        30
        max_mods
        2

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8
        min_pr_mz
        350
        max_pr_mz
        950
        min_fr_mz
        500
        max_fr_mz
        1500
        diann_normalize
        N/A

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DIA
        config_profile_description
        Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A